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Yorodumi- PDB-2ihz: Crystal structure of multifunctional sialyltransferase from paste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ihz | |||||||||
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Title | Crystal structure of multifunctional sialyltransferase from pasteurella multocida with CMP-3F-Neu5Ac and alpha-lactose bound | |||||||||
Components | Alpha-2,3/2,6-sialyltransferase/sialidase | |||||||||
Keywords | TRANSFERASE / sialyltransferase CMP-3F-Neu5Ac / alpha-lactose / two Rossmann domain | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pasteurella multocida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Fisher, A.J. / Ni, L. | |||||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Crystal Structures of Pasteurella multocida Sialyltransferase Complexes with Acceptor and Donor Analogues Reveal Substrate Binding Sites and Catalytic Mechanism. Authors: Ni, L. / Chokhawala, H.A. / Cao, H. / Henning, R. / Ng, L. / Huang, S. / Yu, H. / Chen, X. / Fisher, A.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ihz.cif.gz | 103.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ihz.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ihz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ihz_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2ihz_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2ihz_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 2ihz_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/2ihz ftp://data.pdbj.org/pub/pdb/validation_reports/ih/2ihz | HTTPS FTP |
-Related structure data
Related structure data | 2ihjC 2ihkC 2ilvC 2ex1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46467.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pasteurella multocida (bacteria) / Strain: pm70 / Gene: Pm0188 / Plasmid: pET23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15KI8, EC: 2.4.99.4 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose |
#3: Chemical | ChemComp-CSF / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25% PEG MME 2000, 0.2 M NaBr, 40.4% Triton X-100, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Apr 21, 2006 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→64.94 Å / Num. all: 33299 / Num. obs: 33274 / % possible obs: 99.92 % / Redundancy: 6.18 % / Rsym value: 0.0459 / Net I/σ(I): 10.28 |
Reflection shell | Resolution: 2→2.09 Å / Mean I/σ(I) obs: 2.15 / Rsym value: 0.2107 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EX1 Resolution: 2→63.63 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.411 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.035 Å2
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Refinement step | Cycle: LAST / Resolution: 2→63.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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